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The Norway spruce genome sequence and conifer genome evolution
The draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm, is presented, revealing numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs, which opens up new genomic avenues for conifer forestry and breeding.
Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs
- C. Liewlaksaneeyanawin, C. Ritland, Y. El-Kassaby, K. Ritland
- Biology, Environmental ScienceTheoretical and Applied Genetics
- 26 March 2004
Sequence analyses revealed that the frequencies of insertions/deletions and base substitutions were lower in EST-SSRs than in other types of microsatellites, confirming that EST- SSRs are more conserved than traditional SSRs.
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data
A whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software is described, demonstrating how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity.
Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags
These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.
Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation.
- J. Ehlting, Nathalie Mattheus, C. Douglas
- BiologyThe Plant journal : for cell and molecular…
- 4 April 2005
Global transcript profiling employing an Arabidopsis full-genome longmer microarray revealed candidate genes encoding enzymes that catalyze missing links in the shikimate pathway, namely arogenate dehydrogenase and prephenate aminotransferase.
Proteome analysis of early somatic embryogenesis in Picea glauca
To aid in unravelling the embryo developmental process, two‐dimensional electrophoresis was employed to quantitatively assess the expression levels of proteins across four stages of somatic embryo maturation in white spruce and forty‐eight differentially expressed proteins have been identified.
The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis.
The results are consistent with the prediction that selective constraint is progressively relaxed along metabolic pathways, and a new measure of pathway position, the Pathway Pleiotropy Index (PPI), which counts groups of enzymes between pathway branch points is found to be superior to pathway position in explaining variation in d(N)/d(S) along each pathway.
Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or…
This study provides the first large-scale survey of insect-induced defence transcripts in a gymnosperm and provides a platform for functional investigation of plant-insect interactions in spruce.
Genomics of hybrid poplar (Populus trichocarpa× deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full‐length cDNA libraries, expressed sequence tags, and a…
This study provides the first genome‐scale approach to characterize insect‐induced defences in a woody perennial providing a solid platform for functional investigation of plant–insect interactions in poplar.
Isolation of high-quality RNA from gymnosperm and angiosperm trees.
An improved protocol was developed for efficient and reliable extraction of high-quality total RNA and mRNA from various tissues of spruce and poplar trees, as well as other plant species, and suitable for standard expressed sequence tags (ESTs), full-length cDNA library construction, and for microarray applications.